fix: POSIX compatibility and exit code handling in hooks

CLAUDE.md

@@ -23,12 +23,18 @@ Run these from the `main/` worktree directory:
 ```bash
 just setup          # First-time setup: install dev tools + git hooks
 just test           # Run all tests
+just test-unit      # Run unit tests only
+just test-integration        # Run integration tests (builds first)
+just test-integration-parallel  # Run integration tests in parallel
+just test-match <pattern>    # Run specific test by pattern
+just test-pkg <pkg>          # Run tests for specific package (e.g., git, hooks)
 just lint           # Run go vet + golangci-lint
 just build          # Build to ./bin/
 just build-all      # Cross-platform build check (linux/darwin/windows)
 just dev            # Build and show version
 just clean          # Remove build artifacts and test fixtures
 just fmt            # Format code (go fmt + goimports)
+just setup-test-repo # Set up test repo for integration tests
 ```
 
 Or directly with Go:
@@ -121,7 +127,7 @@ cmd/wt/main.go → commands.Execute()
                    ↓
              rootCmd.Execute() (Cobra)
                    ↓
-         Subcommand (clone, add, list, switch, delete, prune, repair)
+         Subcommand (clone, add, list, switch, delete, prune, repair, config, completion)
                    ↓
          internal/git/* for git operations
                    ↓
@@ -141,6 +147,11 @@ Commands register in `init()` via `rootCmd.AddCommand()`.
 | `internal/config/`        | TOML config loading, hierarchical merge, workflow configs |
 | `internal/ui/`            | Terminal styling (lipgloss) and JSON output envelope      |
 
+**Test structure:**
+
+- `test/integration/` - Integration tests (use `just test-integration`)
+- `internal/*/_test.go` - Unit tests co-located with source
+
 **Key patterns:**
 
 - Branch names with slashes flatten to dashes for directory names (`feature/auth` → `feature-auth`)

internal/commands/config.go

@@ -97,8 +97,14 @@ func runConfigInit(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("failed to create directory: %w", err)
 	}
 
-	// Write config template
-	template := config.GenerateConfigTemplate()
+	// For global config, detect integrations BEFORE generating template
+	var selections config.IntegrationSelections
+	if configGlobal && !IsJSONOutput() {
+		selections = detectIntegrations()
+	}
+
+	// Generate config template with selected integrations
+	template := config.GenerateConfigWithIntegrations(selections)
 	if err := os.WriteFile(configPath, []byte(template), 0644); err != nil {
 		return fmt.Errorf("failed to write config file: %w", err)
 	}
@@ -110,9 +116,9 @@ func runConfigInit(cmd *cobra.Command, args []string) error {
 
 	fmt.Println(ui.SuccessMsg(fmt.Sprintf("Created %s", configPath)))
 
-	// For global config, detect available tools and offer to enable
+	// Show what was enabled
 	if configGlobal {
-		detectAndEnableIntegrations(configPath)
+		printEnabledIntegrations(selections)
 	}
 
 	return nil
@@ -125,8 +131,9 @@ type integration struct {
 	detected    bool
 }
 
-// detectAndEnableIntegrations detects available tools and offers to enable them
-func detectAndEnableIntegrations(configPath string) {
+// detectIntegrations detects available tools and prompts user to select which to enable
+// Returns the user's selections for template generation
+func detectIntegrations() config.IntegrationSelections {
 	// Detect available tools
 	integrations := []integration{
 		{
@@ -155,7 +162,7 @@ func detectAndEnableIntegrations(configPath string) {
 	}
 
 	if len(available) == 0 {
-		return
+		return config.IntegrationSelections{}
 	}
 
 	// Build options for multi-select
@@ -180,61 +187,41 @@ func detectAndEnableIntegrations(configPath string) {
 	).WithKeyMap(DefaultFormKeyMap())
 
 	if err := form.Run(); err != nil {
-		return // User aborted, silently exit
+		return config.IntegrationSelections{} // User aborted
 	}
 
-	// Enable selected integrations
+	// Convert selections to struct
+	var selections config.IntegrationSelections
 	for _, name := range selected {
 		switch name {
 		case "zoxide":
-			enableZoxide(configPath)
+			selections.Zoxide = true
 		case "gh":
-			enableGitHub(configPath)
+			selections.GitHub = true
 		case "direnv":
-			enableDirenv(configPath)
+			selections.Direnv = true
 		}
 	}
+
+	return selections
 }
 
 func isCommandAvailable(name string) bool {
 	_, err := exec.LookPath(name)
 	return err == nil
 }
 
-func enableZoxide(configPath string) {
-	for _, event := range []string{"post_clone", "post_add"} {
-		if err := config.AddHookToConfig(configPath, "zoxide", event); err != nil {
-			fmt.Println(ui.WarningMsg(fmt.Sprintf("Failed to enable zoxide: %v", err)))
-			return
-		}
-	}
-	fmt.Println(ui.SuccessMsg("Enabled zoxide for quick worktree navigation"))
-}
-
-func enableGitHub(configPath string) {
-	// Add gh-default to post_clone for auto-setting default repo
-	if err := config.AddHookToConfig(configPath, "gh-default", "post_clone"); err != nil {
-		fmt.Println(ui.WarningMsg(fmt.Sprintf("Failed to enable gh-default: %v", err)))
-		return
+// printEnabledIntegrations shows the user what integrations were configured
+func printEnabledIntegrations(selections config.IntegrationSelections) {
+	if selections.Zoxide {
+		fmt.Println(ui.SuccessMsg("Enabled zoxide for quick worktree navigation"))
 	}
-
-	// Add github-issue to feature and bugfix workflows
-	for _, workflow := range []string{"feature", "bugfix"} {
-		if err := config.AddWorkflowHook(configPath, workflow, "github-issue", "pre_create"); err != nil {
-			fmt.Println(ui.WarningMsg(fmt.Sprintf("Failed to enable github-issue for %s workflow: %v", workflow, err)))
-			return
-		}
+	if selections.GitHub {
+		fmt.Println(ui.SuccessMsg("Enabled GitHub CLI integration (gh-default, github-issue)"))
 	}
-
-	fmt.Println(ui.SuccessMsg("Enabled GitHub CLI integration (gh-default, github-issue, github-pr)"))
-}
-
-func enableDirenv(configPath string) {
-	if err := config.AddHookToConfig(configPath, "direnv", "post_add"); err != nil {
-		fmt.Println(ui.WarningMsg(fmt.Sprintf("Failed to enable direnv: %v", err)))
-		return
+	if selections.Direnv {
+		fmt.Println(ui.SuccessMsg("Enabled direnv for auto-loading .envrc files"))
 	}
-	fmt.Println(ui.SuccessMsg("Enabled direnv for auto-loading .envrc files"))
 }
 
 func runConfigShow(cmd *cobra.Command, args []string) error {

internal/config/config.go

@@ -48,6 +48,13 @@ func ptrBool(b bool) *bool {
 	return &b
 }
 
+// IntegrationSelections holds the user's selected integrations for config generation
+type IntegrationSelections struct {
+	Zoxide bool
+	GitHub bool
+	Direnv bool
+}
+
 // DefaultConfig returns the default configuration
 func DefaultConfig() *Config {
 	return &Config{
@@ -197,6 +204,20 @@ func Load(path string) (*Config, error) {
 		return nil, err
 	}
 
+	// Restore defaults for zero timeout values (prevents instant timeouts when
+	// users have git_long_timeout = 0 in their config, which was a common issue
+	// from copying the config template without editing)
+	defaults := DefaultConfig()
+	if cfg.GitTimeout == 0 {
+		cfg.GitTimeout = defaults.GitTimeout
+	}
+	if cfg.GitLongTimeout == 0 {
+		cfg.GitLongTimeout = defaults.GitLongTimeout
+	}
+	if cfg.HookTimeout == 0 {
+		cfg.HookTimeout = defaults.HookTimeout
+	}
+
 	return cfg, nil
 }
 
@@ -572,9 +593,15 @@ func removeFromSlice(slice []string, item string) []string {
 
 // GenerateConfigTemplate returns a config file template with all options commented
 func GenerateConfigTemplate() string {
-	return `# ============================================================
+	return GenerateConfigWithIntegrations(IntegrationSelections{})
+}
+
+// GenerateConfigWithIntegrations returns a config template with selected integrations pre-configured
+func GenerateConfigWithIntegrations(selections IntegrationSelections) string {
+	// Build the base template (settings section)
+	template := `# ============================================================
 # wt configuration
-# Generated by: git wt config init
+# Generated by: wt config init
 # Uncomment and modify options as needed
 # ============================================================
 
@@ -628,13 +655,132 @@ func GenerateConfigTemplate() string {
 # Flag: --hook-timeout
 # hook_timeout = 30
 
-# --- Hooks ---
-# Shell commands to run after operations
+`
+
+	// Build hooks section based on selections
+	template += generateHooksSection(selections)
+
+	// Build workflows section if GitHub is enabled
+	if selections.GitHub {
+		template += generateWorkflowsSection(selections)
+	}
+
+	return template
+}
+
+// generateHooksSection creates the hooks section of the config template
+func generateHooksSection(selections IntegrationSelections) string {
+	hasAnyHook := selections.Zoxide || selections.GitHub || selections.Direnv
+
+	if !hasAnyHook {
+		// No integrations selected - show commented template
+		return `# --- Hooks ---
+# Shell commands or bundled hook names to run after operations
 # Environment variables: WT_PATH, WT_BRANCH, WT_PROJECT_ROOT, WT_DEFAULT_BRANCH
-# Template variables: {{.Path}}, {{.Branch}}, {{.ProjectRoot}}, {{.DefaultBranch}}
+# Available hooks: zoxide, gh-default, direnv, github-issue, github-pr
+# Run 'wt hooks list' to see all available hooks
 
 # [hooks]
 # post_clone = []
 # post_add = []
 `
+	}
+
+	// Build hook arrays
+	var postClone, postAdd []string
+
+	if selections.Zoxide {
+		postClone = append(postClone, "zoxide")
+		postAdd = append(postAdd, "zoxide")
+	}
+	if selections.GitHub {
+		postClone = append(postClone, "gh-default")
+	}
+	if selections.Direnv {
+		postAdd = append(postAdd, "direnv")
+	}
+
+	section := `# --- Hooks ---
+# Shell commands or bundled hook names to run after operations
+# Environment variables: WT_PATH, WT_BRANCH, WT_PROJECT_ROOT, WT_DEFAULT_BRANCH
+# Available hooks: zoxide, gh-default, direnv, github-issue, github-pr
+# Run 'wt hooks list' to see all available hooks
+
+[hooks]
+`
+
+	// Format post_clone
+	section += "# Runs after cloning a repository (wt clone)\n"
+	section += fmt.Sprintf("post_clone = %s\n\n", formatStringSlice(postClone))
+
+	// Format post_add
+	section += "# Runs after creating a new worktree (wt add/new)\n"
+	section += fmt.Sprintf("post_add = %s\n", formatStringSlice(postAdd))
+
+	return section
+}
+
+// generateWorkflowsSection creates the workflows section for GitHub integration
+func generateWorkflowsSection(selections IntegrationSelections) string {
+	// Build post_add hooks for workflows
+	var workflowPostAdd []string
+	if selections.Direnv {
+		workflowPostAdd = append(workflowPostAdd, "direnv")
+	}
+	if selections.Zoxide {
+		workflowPostAdd = append(workflowPostAdd, "zoxide")
+	}
+
+	section := `
+# --- Workflows ---
+# Predefined branch naming and hook configurations
+# Use with: wt new --workflow=feature "my feature"
+# Or use shortcuts: wt new --issue 123, wt new --pr 456
+
+[workflows.feature]
+# For new feature development
+description = "New feature development"
+branch_template = "feat/{slug}"
+[workflows.feature.hooks]
+# Prompts for GitHub issue to link (optional)
+pre_create = ["github-issue"]
+`
+	section += fmt.Sprintf("post_add = %s\n", formatStringSlice(workflowPostAdd))
+
+	section += `
+[workflows.bugfix]
+# For bug fixes
+description = "Bug fix"
+branch_template = "fix/{slug}"
+[workflows.bugfix.hooks]
+# Prompts for GitHub issue to link (optional)
+pre_create = ["github-issue"]
+`
+	section += fmt.Sprintf("post_add = %s\n", formatStringSlice(workflowPostAdd))
+
+	return section
+}
+
+// formatStringSlice formats a string slice as a TOML array
+func formatStringSlice(s []string) string {
+	if len(s) == 0 {
+		return "[]"
+	}
+	quoted := make([]string, len(s))
+	for i, v := range s {
+		quoted[i] = fmt.Sprintf("%q", v)
+	}
+	return "[" + joinStrings(quoted, ", ") + "]"
+}
+
+// joinStrings joins strings with a separator (avoiding strings import for this simple case)
+func joinStrings(s []string, sep string) string {
+	if len(s) == 0 {
+		return ""
+	}
+	result := s[0]
+	for i := 1; i < len(s); i++ {
+		result += sep + s[i]
+	}
+	return result
 }